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Find Candidate ORFs

Source: R/orf_finder.R
find_candidate_orfs.Rd

Identify candidate open reading frames (ORFs) based on entropy analysis and sequence features.

Usage

find_candidate_orfs(
  sequence,
  scan_result,
  peaks,
  min_orf_length = 90,
  start_codons = c("ATG"),
  stop_codons = c("TAA", "TAG", "TGA")
)

Arguments

sequence

Character string or DNAString object representing DNA sequence

scan_result

Data frame from sliding_window_scan()

peaks

Data frame from entropy_peak_detection()

min_orf_length

Minimum ORF length in base pairs (default: 90, i.e., 30 aa)

start_codons

Character vector of valid start codons (default: c("ATG"))

stop_codons

Character vector of stop codons (default: c("TAA", "TAG", "TGA"))

Value

Data frame with candidate ORF information

Examples

sequence <- paste(rep("ATGATGATGTTATTATTACGCCGCCGCC", 20), collapse = "")
result <- sliding_window_scan(sequence, window_size = 150, step_size = 30)
peaks <- entropy_peak_detection(result, threshold = 0.1)
#> Warning: No peaks detected with current threshold
candidates <- find_candidate_orfs(sequence, result, peaks)
#> Warning: No peaks provided, returning empty data frame